Save Custom Layout in Blender 2.67b?
The User preferences such as addons have been separated from the startup .blend in Blender 2.66

So as of Blender 2.66 clicking "save user settings" in the User Preferences menu will only save settings such as enabled addons, themes, shortcuts/hotkeys, etc..


To save the current blendfile (includes layout(s)/materals/models/settings etc.. Pretty much everything.)  as the startup .blend, press Ctrl+U and click "save startup .blend" (Note that this includes User Preference settings)  
To save a different screen layout so it is accessible in the selector at the top of the window,

  

Press the + to the right of the drop down selector, Arrange the screen the way you want it, then name it whatever you want. (Note that to have it defaulted when you start Blender you then have to save the startup .blend (Ctrl+U)